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In many molecular biology animations, a molecule just flies in and goes straight to the right spot. It's clearly a useful simplification, but I'm interested in learning more of the full story.

  • I guess at short distances the electric polarizations of the molecules pull them into the right spot. But I have no idea what is "short" here, on the scale of these animations.
  • This all is not happening in vacuum. There must be a lot of other molecules crowding around. (Water at least.) How does all that not clog up these mechanisms? I imagine an ATP synthase accidentally sucking in a stray RNA strand.
  • I understand the animations are also slowed down a lot, foiling my intuition. Do the molecules just randomly bump into each other SO MUCH that hundreds of times per second an ADP randomly flies into the synthase?

Animation of an ATP synthase with ADP molecules flying in:

ATP synthase animation

Source: http://www.mrc-mbu.cam.ac.uk/projects/2245/atp-synthase

Animation of a DNA polymerase with green donuts (DNA primases?) flying in:

DNA polymerase animation

Source: https://dnalc.cshl.edu/resources/3d/04-mechanism-of-replication-advanced.html

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    $\begingroup$ Apologies for the childish question! I don't know if it's okay to ask such here. $\endgroup$ Sep 8, 2021 at 6:22
  • $\begingroup$ I'm trying to think through the third point. I read that molecules in room temperature water have speeds around 500 m/s. So they can cross a 50 nm distance (roughly the width of these GIFs I think) 10 billion times in a second. The movement of the arriving molecule is much slowed down then. $\endgroup$ Sep 8, 2021 at 6:28
  • $\begingroup$ Another number! The mean free path in air is around 70 nm. In water, 0.2 nm. They indeed are bumping into each other a lot! $\endgroup$ Sep 8, 2021 at 8:33
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    $\begingroup$ I am voting to close this question as a duplicate of the following: Molecular animations of, say, protein synthesis, are simplified, but how exactly?. This is another related question worth consulting. $\endgroup$
    – David
    Sep 8, 2021 at 9:23
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    $\begingroup$ You should be aware that the only aspect of such animations that is based on experimental structure determination is the representation of the proteins and associated parts of the nucleic acids. The movement of the proteins is extrapolated from "still" images and the movement of small molecules is completely invented. $\endgroup$
    – David
    Sep 8, 2021 at 9:29

1 Answer 1

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It depends on the molecule and the type of a chemical reaction. In simple chemical reactions molecules literally randomly collide with the probability proportional to their concentrations, which gives rise to the law of mass action.

However, in a cell, in addition to simple diffusion of the molecules, there are also means of directional transport of molecules from one place to another, such as membrane transport, transport by motor proteins, etc.

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    $\begingroup$ I'd add something about concentration gradients to the simple diffusion part. $\endgroup$
    – bob1
    Sep 8, 2021 at 8:22
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    $\begingroup$ Thank you! Good point about the law of mass action. When something is burning, I don't go thinking "how do the oxygen molecules find their way precisely into this reaction". I guess as long as the concentration is high enough, random collisions are good enough. Like for ATP? And for rare or unique molecules we have transport molecules. $\endgroup$ Sep 8, 2021 at 8:30
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    $\begingroup$ @DanielDarabos when something is burning a big part is played by convection - the hot air containing the products of burning (CO, CO2) rises, and the fresh air, rich in oxygen, is sucked in. This is not the same as diffusion, which is random motion of molecules. Also, bob1 in their comment above probably meant the osmosis - which is another mechanism of transport governed by concentration difference. $\endgroup$ Sep 8, 2021 at 8:54
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    $\begingroup$ @RogerVadim There's still a lot of diffusion happening at a local scale in that scenario as far as interactions among molecules; the convection portion is best understood as the mechanism for keeping the concentration reasonably high rather than depleting. An important analogy in biology would be the distinction between mass flow, like blood moving in blood vessels, and the diffusion processes by which nutrients/oxygen in blood actually make it into cells. $\endgroup$
    – Bryan Krause
    Sep 8, 2021 at 14:11
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    $\begingroup$ @RogerVadim "I also agree that diffusion plays a role in fire" - right, this was my main motivation for commenting. I think your first comment here about convection could have been misinterpreted by someone else (OP in particular) to think that diffusion wasn't as important there. Yes, convection is important in fire, but they were correct to think about the "diffusion part" that matches up molecules for chemical reactions to be effectively the same in combustion/fire and in a cell, and I didn't want them walking away thinking these were fundamentally different. $\endgroup$
    – Bryan Krause
    Sep 8, 2021 at 14:35

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